Variant report

Variant	rs9609681
Chromosome Location	chr22:33419847-33419848
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000232218	Chromatin interaction
ENSG00000100150	Chromatin interaction
ENSG00000243519	Chromatin interaction
ENSG00000205853	Chromatin interaction
ENSG00000241954	Chromatin interaction
ENSG00000185666	Chromatin interaction
ENSG00000205856	Chromatin interaction
ENSG00000230736	Chromatin interaction
ENSG00000128276	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs13054969	0.81[CHB][hapmap]
rs916396	0.82[CHB][hapmap]
rs9607002	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9607007	0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9609654	0.83[CHB][hapmap]
rs9609656	0.82[CHB][hapmap]
rs9609678	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes]
rs9609680	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9609688	0.82[JPT][hapmap]
rs9609689	0.84[GIH][hapmap];0.82[JPT][hapmap]
rs9609695	0.85[JPT][hapmap]
rs9609696	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531568	chr22:33336868-33480272	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv531587	chr22:33346710-33809338	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv948523	chr22:33414164-34098417	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9609681	GATSL3	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33403000-33420000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr22:33414400-33420600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr22:33414800-33422000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr22:33414800-33430600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr22:33415000-33434200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr22:33415800-33421800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr22:33417200-33424200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr22:33417400-33430800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr22:33417800-33421800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr22:33418400-33430600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr22:33418600-33420200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr22:33419200-33424000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr22:33419400-33423000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr22:33419600-33420200	Enhancers	Right Atrium	heart

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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